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StrAl is an alignment tool designed to provide multiple alignments of non-coding RNAs following a fast progressive strategy. It combines the thermodynamic base pairing information derived from RNAfold calculations in the form of base pairing probability vectors with the information of the primary sequence. Thus the scoring system is composed of two major parts evaluating the given structural and the sequence information, respectively. We apply an affine gap weight model to our scoring system, which also allows for weighting the structure evaluation against the sequence evaluation through the factor α. For an in-depth description of our algorithm see the publication listed below.


The StrAl webservice can handle nearly all of the common alignment formats. If you wish to alter some of the programs' parameters please use the advanced submission form. Here you are able to choose from different guide tree methods and to adjust gap penalty values as well as the structure weighting factor α. Currently the service is restricted to alignments consisting of 50 sequences maximum with an average length of 500nt.


  • secis methanococcus
  • Please avoid non-alphanumerical signs, e.g. dots(.) in the annotation line.

    Project Team

    Institut für Physikalische Biologie
    Heinrich-Heine-Universität Düsseldorf
    Universitätsstraße 1, Gebäude 26.12.U1
    D-40225 Düsseldorf
    Prof. Dr. Gerhard Steger
    Phone: +49-211-81-14597
    Fax: +49-211-81-15167
    For further requests, bug reporting, etc. contact stral@biophys.uni-duesseldorf.de.


  • Dalli, D., Wilm, A., Mainz, I., Steger, G. (2006). StrAl: Progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. Bioinformatics [ doi:10.1093/bioinformatics/btl142 supplement].

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